{"id":19434492,"url":"https://github.com/mlin/phylocsf","last_synced_at":"2025-04-24T20:32:07.413Z","repository":{"id":138431537,"uuid":"836378","full_name":"mlin/PhyloCSF","owner":"mlin","description":"Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions","archived":false,"fork":false,"pushed_at":"2023-10-16T15:11:59.000Z","size":33138,"stargazers_count":65,"open_issues_count":17,"forks_count":24,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-04-03T10:37:58.979Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://compbio.mit.edu/PhyloCSF","language":"OCaml","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"agpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mlin.png","metadata":{"files":{"readme":"README","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2010-08-13T18:24:30.000Z","updated_at":"2025-02-26T02:28:02.000Z","dependencies_parsed_at":null,"dependency_job_id":"c6d2ee19-3214-4458-957c-cc23a2ea3dec","html_url":"https://github.com/mlin/PhyloCSF","commit_stats":null,"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlin%2FPhyloCSF","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlin%2FPhyloCSF/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlin%2FPhyloCSF/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlin%2FPhyloCSF/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mlin","download_url":"https://codeload.github.com/mlin/PhyloCSF/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250704830,"owners_count":21473769,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-10T14:46:36.705Z","updated_at":"2025-04-24T20:32:07.059Z","avatar_url":"https://github.com/mlin.png","language":"OCaml","funding_links":[],"categories":[],"sub_categories":[],"readme":"  +---------------------------------------------------------------------+\n  |             ____  __          __       ___________ ______           |\n  |            / __ \\/ /_  __  __/ /____  / ____/ ___// ____/           |\n  |           / /_/ / __ \\/ / / / // __ \\/ /    \\__ \\/ /_               |\n  |          / ____/ / / / /_/ / // /_/ / /___ ___/ / __/               |\n  |         /_/   /_/ /_/\\__, /_/ \\____/\\____//____/_/                  |\n  |                      /____/                                         |\n  |                                                                     |\n  |                 http://compbio.mit.edu/PhyloCSF                     | \n  +---------------------------------------------------------------------+\n\nSOURCE DISTRIBUTION\n\nPlease see our web site for more information about PhyloCSF and how to use it.\nPhyloCSF is written in OCaml. This source distribution is divided into a\nlibrary, CamlPaml, containing generic infrastructure for phylogenetic rate\nmodels, and a program implementing the PhyloCSF-specific models and driver\nprogram. With additional development, the CamlPaml library will eventually be\nreleased as a separate entity, but for now it is just part of this\ndistribution.\n\nHere are the steps to build the source:\n\n[1] Install the OCaml package manager OPAM\n\nhttp://opam.ocamlpro.com/doc/Quick_Install.html\n\nThis will install a minimal OCaml toolchain (if not already present on your\nsystem) and the OPAM package manager. Once it's installed, initialize your\nshell environment by running: eval $(opam config env)\n\n[2] Install dependencies using OPAM\n\nopam install batteries ocaml+twt gsl\n\nThe gsl package may require you to separately install the GNU Scientific\nLibrary (GSL) from: http://www.gnu.org/software/gsl/\nOn Debian/Ubuntu systems GSL is available in the 'libgsl0-dev' package, and on\nMac OS X, 'gsl' is available in both Homebrew and MacPorts.\n\n[3] Compile PhyloCSF\n\nNow just run 'make' in this directory. This will build and install the\nCamlPaml library, then compile the PhyloCSF executable and copy it to\nthis directory. You can then use the ./PhyloCSF dispatch script like the\nexamples found on our website, e.g.\n\n./PhyloCSF 12flies PhyloCSF_Examples/tal-AA.fa\n\nPhyloCSF should be usable in this way by anyone on the machine/cluster with rx\npermissions; they don't have to set up OPAM or anything else. PhyloCSF can\nbe started from any working directory.\n\nIf you want to 'install' PhyloCSF somewhere, you must transplant PhyloCSF,\nPhyloCSF.ARCH (where e.g. ARCH=Linux.x86_64), and the PhyloCSF_Parameters\ndirectory to the desired location.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmlin%2Fphylocsf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmlin%2Fphylocsf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmlin%2Fphylocsf/lists"}